A late stoppage time winner from Isaac Fletcher secured Boro's Under-18s their first points of 2020.
Mark Tinkler's young charges came from 1-0 down to lead heading into the final quarter of an hour, but it appeared as though the spoils would be shared when Blackburn Rovers levelled late on.
But there was another twist in the tail deep into second half stoppage time as Fletcher popped up with the winner for Boro to seal their first win of the year.
Sam Burns gave Rovers the lead with just under 20 minutes played, and Boro responded in the second period just after the hour mark as Callum Cavanagh equalised.
Heading into the final quarter of an hour, the Teessiders nudged in front courtesy of Isiah Cornet, however Blackburn looked to have rescued a point in the final minute of normal time when Chanka Zimba netted to restore parity.
But Boro had the final say in a dramatic final few minutes at Brockhall, as Fletcher was on hand to score and to bag our U18s' first win of the year.
Boro's U18s are on the road again next weekend as they travel to Manchester City on Saturday February 1 (12.30pm).
Boro: Metcalfe, Gibson, Beals, Hannah, Marshall, Cornet, Sykes, Waites, Cavanagh, Balde, Green. Subs: Flatters, Fletcher, Stott, Reed, Lindo.